Related papers: Insular microbiogeography
According to the universally accepted concept of the development of life on the Earth, multicellular organisms initially emerged as a result of either the union of identical unicellular organisms with the following functional…
Quantitative methods for studying biodiversity have been traditionally rooted in the classical theory of finite frequency tables analysis. However, with the help of modern experimental tools, like high throughput sequencing, we now begin to…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
How diversity is maintained in natural ecosystems is a long-standing question in Theoretical Ecology. By studying a system that combines ecological dynamics, heterogeneous interactions and spatial structure, we uncover a new mechanism for…
Macroevolutionary dynamics often display sudden, explosive surges, where systems remain relatively stable for extended periods before experiencing dramatic acceleration that frequently exceeds traditional exponential growth. This pattern is…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Recent advances in metagenomics have revealed macroecological patterns or "laws" describing robust statistical regularities across microbial communities. Stochastic logistic models (SLMs), which treat species as independent -- akin to ideal…
Understanding the causes and effects of spatial vegetation patterns is a fundamental problem in ecology, especially because these can be used as early predictors of catastrophic shifts such as desertification processes. Empirical studies of…
Qian, Luscombe and Gerstein [J. Molecular Biol. 313 (2001) 673--681] introduced a model of the diversification of protein folds in a genome that we may formulate as follows. Consider a multitype Yule process starting with one individual in…
We investigate the formation of stable ecological networks where many species share the same resource. We show that such stable ecosystem naturally occurs as a result of extinctions. We obtain an analytical relation for the number of…
Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or sets of metrics depend on the context and…
We propose a model of multispecies populations surviving on distributed resources. System dynamics are investigated under changes in abiotic factors such as the climate, as parameterized through environmental temperature. In particular, we…
Biodiversity widely observed in ecological systems is attributed to the dynamical balance among the competing species. The time-varying populations of the interacting species are often captured rather well by a set of deterministic…
In this paper we suggest that, under suitable conditions, supervised learning can provide the basis to formulate at the microscopic level quantitative questions on the phenotype structure of multicellular organisms. The problem of…
One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species…
Explaining biodiversity is a fundamental issue in ecology. A long-standing puzzle lies in the paradox of the plankton: many species of plankton feeding on a limited variety of resources coexist, apparently flouting the competitive exclusion…
The relationship between the dynamics of a community and its constituent pairwise interactions is a fundamental problem in ecology. Higher-order ecological effects beyond pairwise interactions may be key to complex ecosystems, but…